Contacts of the helix formed by residues 438 - 443 (chain A) in PDB entry 4IDT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 438 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ALA* 3.6 28.3 - - + +
358A LYS* 4.0 9.6 - - + +
361A ALA* 3.7 10.7 - - + +
436A PHE* 3.7 14.6 - - - -
437A ARG* 1.3 71.4 - - - +
439A GLU* 1.3 61.5 + - - +
440A GLU 3.0 0.2 - - - -
441A LEU* 2.8 23.2 + - - +
442A MET* 2.9 31.7 + - - +
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Residues in contact with GLU 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A ARG* 3.1 31.9 + - - +
438A ALA* 1.3 84.5 + - - +
440A GLU* 1.3 61.7 + - - +
441A LEU 3.0 1.3 + - - -
442A MET* 3.8 15.5 - - + -
443A ALA* 3.0 26.9 + - - +
535A PHE* 4.0 3.5 - - - +
538A ALA* 3.4 28.7 - - + +
539A VAL* 4.2 11.3 - - - +
540A CYS* 4.3 18.8 + - + +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A PHE* 4.2 16.5 - - - +
429A LYS* 2.4 38.6 + - - -
431A VAL* 4.5 5.5 - - - +
435A VAL 5.7 0.2 - - - +
436A PHE* 4.2 6.8 - - + -
437A ARG* 2.9 25.1 + - + +
439A GLU* 1.3 78.3 - - - +
441A LEU* 1.3 58.8 + - - +
444A CYS* 3.5 18.0 - - - -
467A ILE* 3.3 27.3 - - + +
534A ASP* 3.1 9.0 - - - +
535A PHE* 3.7 21.3 + - - +
536A GLY* 3.2 21.9 + - - -
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Residues in contact with LEU 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A LEU* 3.8 21.3 - - + -
354A THR* 4.8 2.5 - - - +
357A ALA* 3.9 21.3 - - + -
360A TRP* 4.0 3.8 - - + -
436A PHE* 3.9 18.6 - - + -
438A ALA 2.8 5.7 + - - +
440A GLU* 1.3 83.3 - - - +
442A MET* 1.3 58.4 + - + +
443A ALA 3.1 2.5 - - - -
444A CYS* 3.4 3.3 + - - -
445A ALA* 2.9 37.7 + - + +
455A LEU* 4.0 16.8 - - + +
458A ALA* 3.5 26.2 - - + -
467A ILE* 3.5 38.6 - - + -
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Residues in contact with MET 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A THR* 3.8 34.6 + - + +
357A ALA* 5.4 0.7 - - + -
358A LYS* 3.5 31.9 - - - +
438A ALA* 2.9 38.9 + - + +
439A GLU* 3.4 14.6 + - + -
441A LEU* 1.3 78.0 - - - +
443A ALA* 1.3 58.1 + - - +
444A CYS 3.7 0.3 + - - -
445A ALA* 4.3 5.5 + - - +
447A LEU* 5.6 1.6 - - - +
511A ILE* 4.4 7.1 - - - +
540A CYS* 4.0 29.6 - - + -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A GLU 3.0 19.0 + - - +
442A MET* 1.3 77.3 - - - +
444A CYS* 1.3 58.7 + - - +
447A LEU* 3.1 19.4 - - - +
506A LEU* 3.7 8.5 - - - +
511A ILE* 3.5 25.1 - - + +
535A PHE* 3.4 24.6 - - + -
538A ALA* 3.7 14.6 - - + -
540A CYS* 4.7 6.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il